X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3H4E 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5290PEG550MME (13-14%), KSCN (0.15M), TRIS (0.1M, pH 8.5), 10mM dATP
Crystal Properties
Matthews coefficientSolvent content
2.6553.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.81α = 90
b = 90.81β = 90
c = 56.68γ = 120
Symmetry
Space GroupP 6

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2014-09-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.0345.9894.90.1120.0770.9938.22.916259
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.032.0869.10.5510.4180.421.92.4877

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3H4E2.0445.981548876995.420.23730.23590.2632RANDOM26.365
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.190.090.19-0.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.805
r_dihedral_angle_4_deg13.086
r_dihedral_angle_3_deg10.603
r_dihedral_angle_1_deg4.762
r_mcangle_it2.957
r_mcbond_it1.763
r_mcbond_other1.756
r_angle_refined_deg0.991
r_angle_other_deg0.864
r_chiral_restr0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.805
r_dihedral_angle_4_deg13.086
r_dihedral_angle_3_deg10.603
r_dihedral_angle_1_deg4.762
r_mcangle_it2.957
r_mcbond_it1.763
r_mcbond_other1.756
r_angle_refined_deg0.991
r_angle_other_deg0.864
r_chiral_restr0.05
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1551
Nucleic Acid Atoms
Solvent Atoms82
Heterogen Atoms13

Software

Software
Software NamePurpose
MAR345dtbdata collection
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction